The Ecuador-Colombia Conflict
What happened?
On October 5, 2008, a serious violation of national soveriengty was taken place when Colombia government forces crossed the border into Ecuador to conduct a deadly assault against the Revolutionary Armed Forces of Colombia (FARC) rebel camp over the weekend. Colombia's government says Venezuela and Ecuador have secretly supported Colombian rebels. Ecuador's government is furious over the military raid and with Venezuela, took their case to the diplomatic front seeking international condemnation for Colombia's deadly assault on the rebel camp.
http://www.foxnews.com/story/0,2933,335073,00.html

Aftermath?
Both countries have severely increased their security focused especially on the borders as this does pertain to a sovereignty issue. The conflict between Colombia and Ecuador ultimately centers around two core issues: Colombia, internally positive that the FARC has been pushed to a breaking point, is focused on security. Colombia wants to ensure that the FARC does not gain a stronghold at the border with Ecuador as it is being uprooted from within the country. Ecuador is focused on the issue of sovereignty. It does not want to become involved in Colombia’s internal conflict, and it wants a clear repudiation of the "terror has no borders" ideology that justified Colombia’s incursion into Ecuador. The primacy of these issues domestically,security in Colombia and sovereignty in Ecuador,means that both countries are treading extra carefully to avoid any missteps that would appear as concessions or capitulations.

Getting Better?
On October 9, 2009, foreign ministers form both Colombia and Ecuador have met to discuss improving relations between their countries. This meeting marked a dramatic change of heart and the effort to improve bilateral relationship ultimately leading to an increased cooperation on security issues. Currently however, their mutual borders continues to be insecure.
http://www.stratfor.com/analysis/20091009_colombia_ecuador_thawing_relations